[gmx-users] RE : gmx-users Digest, Vol 69, Issue 132
ABEL Stephane 175950
Stephane.ABEL at cea.fr
Tue Jan 26 22:54:36 CET 2010
Thanks Justin
Indeed, It worked !!!
In french, one says: "je ne dormirai pas idiot ce soir".
Stéphane
>Thank you Roland for your response
>I have effectively downloaded from the
>http://repo.or.cz/w/gromacs.git/snapshot/HEAD.tar.gz, the HEAD version
>of gmx Unfortunately, the unpacked directory does not contain a
>configure file, I have only an configure.ac.
>So my question is: how to obtain a fully fonctional version of 4.1
>without using git
>Thank you for your response
>
> Hi,
>
> there is currently no web-interface on the official git server. Thus
> repo.or.wz is probably the best solution.
> I checked that http://repo.or.cz/w/gromacs.git/snapshot/HEAD.tar.gz is
> up-to-date.
>
> Roland
>
> On Tue, Feb 23, 2010 at 8:31 AM, intra\sa175950 <stephane.abel at cea.fr>wrote:
>
>
>> Hi all,
>>
>>
>>
>> For a future project, I would like to use gromacs for simulations with the
>> CHARMM force field. I am aware that the CHARMM ff is not yet "officially"
>> supported by gromacs, even if a paper about this port will be published
>> soon. By reading the mailing list, I understand that a beta version of
>> gmx4.1 is available for testing from the git depositary. I have tried to use
>> git, but since I am behind a firewall, I cannot easily access to the
>> depositary. I have tried to obtain a previous from
>> http://repo.or.cz/w/gromacs.git through the master branch but I am not
>> sure that the file downloaded was the latest version. Therefore, my question
>> is how to obtain the latest version of pre gmx4.1 without using git ?
>>
>>
>>
>> Thank you for your help
>>
>>
>>
>> Stéphane
>>
>> --
>> gmx-users mailing list gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>
>
>
>
------------------------------
Message: 3
Date: Tue, 26 Jan 2010 14:00:00 -0500
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Subject: Re: [gmx-users] Re: Obtain a pre-version of gromacs 4.1
without git
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4B5F3BB0.1000801 at vt.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed
Stephane Abel wrote:
> Thank you Roland for your response
>
> I have effectively downloaded from the
> http://repo.or.cz/w/gromacs.git/snapshot/HEAD.tar.gz, the HEAD version
> of gmx Unfortunately, the unpacked directory does not contain a
> configure file, I have only an configure.ac.
>
> So my question is: how to obtain a fully fonctional version of 4.1
> without using git
>
In the code you downloaded, there should be a script called "bootstrap" which
you can execute to generate the configure file.
-Justin
> Thank you for your response
>>
>> Hi,
>>
>> there is currently no web-interface on the official git server. Thus
>> repo.or.wz is probably the best solution.
>> I checked that http://repo.or.cz/w/gromacs.git/snapshot/HEAD.tar.gz is
>> up-to-date.
>>
>> Roland
>>
>> On Tue, Feb 23, 2010 at 8:31 AM, intra\sa175950
>> <stephane.abel at cea.fr>wrote:
>>
>>
>>> Hi all,
>>>
>>>
>>>
>>> For a future project, I would like to use gromacs for simulations
>>> with the
>>> CHARMM force field. I am aware that the CHARMM ff is not yet
>>> "officially"
>>> supported by gromacs, even if a paper about this port will be published
>>> soon. By reading the mailing list, I understand that a beta version of
>>> gmx4.1 is available for testing from the git depositary. I have tried
>>> to use
>>> git, but since I am behind a firewall, I cannot easily access to the
>>> depositary. I have tried to obtain a previous from
>>> http://repo.or.cz/w/gromacs.git through the master branch but I am not
>>> sure that the file downloaded was the latest version. Therefore, my
>>> question
>>> is how to obtain the latest version of pre gmx4.1 without using git ?
>>>
>>>
>>>
>>> Thank you for your help
>>>
>>>
>>>
>>> Stéphane
>>>
>>> --
>>> gmx-users mailing list gmx-users at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/search before
>>> posting!
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>>>
>>
>>
>>
>>
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
------------------------------
Message: 4
Date: Wed, 27 Jan 2010 08:09:47 +1100
From: "Dallas B. Warren" <Dallas.Warren at pharm.monash.edu.au>
Subject: RE: [gmx-users] Ligand coming out while trying Drug-enzyme
tutorial
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID:
<89907EA1DCFB7548A431C13A270F9DD508FD800E at prk-exch-01.vcp.local>
Content-Type: text/plain; charset="us-ascii"
So, what EXACTLY are you doing?
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at pharm.monash.edu.au
+61 3 9903 9167
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble
a nail.
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of vivek sharma
Sent: Monday, 25 January 2010 7:38 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Ligand coming out while trying Drug-enzyme
tutorial
HI Tsjerk,
Thanks for your reply. But, I can't see if it is going suddenly or
gradually.
What i can see is the ligand is away from the molecule after editing the
gro file with PRODRG output.
It seems liek PRODRG has modified the co-ordinates that places ligand
away from the protein.
~Vivek
2010/1/25 Tsjerk Wassenaar <tsjerkw at gmail.com>
Hi Vivek,
> Now when I am processing the modified .gro file to generate box, the
ligand
> and cofactor are going away from the protein molecule and I am not
able to
> analyze the complex.
Gradually going away, or suddenly jumping?
In the latter case, read up on periodic boundary conditions.
Tsjerk
--
Tsjerk A. Wassenaar, Ph.D.
Computational Chemist
Medicinal Chemist
Neuropharmacologist
--
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Message: 5
Date: Tue, 26 Jan 2010 16:26:09 -0500
From: Miguel Quiliano Meza <rifaximina at gmail.com>
Subject: [gmx-users] the solvent group SOL is not continuous
To: gmx-users at gromacs.org
Message-ID:
<6c2f55e31001261326w7d3a2588wf577aa5b3f6614a3 at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
*Hi everyone.
I have a problem when I try to run GENION, GROMACS says:
*
WARNING: turning of free energy, will use lambda=0
Reading file 1x8a_solvatada.tpr, VERSION 3.3.3 (single precision)
Using a coulomb cut-off of 0.9 nm
Will try to add 0 Na ions and 15 NA+ ions.
Select a continuous group of solvent molecules
Opening library file /usr/share/gromacs/top/
aminoacids.dat
Group 0 ( System) has 275439 elements
Group 1 ( Protein) has 1722 elements
Group 2 ( Protein-H) has 1371 elements
Group 3 ( C-alpha) has 185 elements
Group 4 ( Backbone) has 555 elements
Group 5 ( MainChain) has 741 elements
Group 6 (MainChain+Cb) has 909 elements
Group 7 ( MainChain+H) has 921 elements
Group 8 ( SideChain) has 801 elements
Group 9 ( SideChain-H) has 630 elements
Group 10 ( Prot-Masses) has 1722 elements
Group 11 ( Non-Protein) has 273717 elements
Group 12 ( ZN) has 1 elements
Group 13 ( SOL) has 273702 elements
Group 14 ( LIG) has 14 elements
Group 15 ( Other) has 273717 elements
Select a group: 13
Selected 13: 'SOL'
-------------------------------------------------------
Program genion, VERSION 3.3.3
Source code file: ../../../../src/tools/gmx_genion.c, line: 429
Fatal error:
The solvent group SOL is not continuous: index[9]=1732, index[10]=1747
-------------------------------------------------------
"Bad As This Shit Is, This Shit Ain't As Bad As You Think It Is." (Jackie
Brown)
*I do not know the reason,the number of residues in top file and pdb file
are the same. The only warning that I saw was when I ran grompp:
*
WARNING 1 [file 1x8a.top, line unknown]:
The largest charge group contains 11 atoms.
Since atoms only see each other when the centers of geometry of the charge
groups they belong to are within the cut-off distance, too large charge
groups can lead to serious cut-off artifacts.
For efficiency and accuracy, charge group should consist of a few atoms.
For all-atom force fields use: CH3, CH2, CH, NH2 NH, OH, CO2, CO, etc.
*Coincidentally they are some of the atomos of my ligand*
*
I have been reading the web and no-one says nothing about it. I would be
very grateful if someone can help me or give me advices.
Best Regards
MIguel Quiliano*
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